Статті в журналах: "Meta-barcoding"

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Keller, Alexander, Sonja Hohlfeld, Andreas Kolter, Jörg Schultz, Birgit Gemeinholzer, and Markus J. Ankenbrand. "BCdatabaser: on-the-fly reference database creation for (meta-)barcoding." Bioinformatics 36, no. 8 (January 6, 2020): 2630–31. http://dx.doi.org/10.1093/bioinformatics/btz960.

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Abstract Summary DNA barcoding and meta-barcoding have become irreplaceable in research and applications, where identification of taxa alone or within a mixture, respectively, becomes relevant. Pioneering studies were in the microbiological context, yet nowadays also plants and animals become targeted. Given the variety of markers used, formatting requirements for classifiers and constant growth of primary databases, there is a need for dedicated reference database creation. We developed a web and command-line interface to generate such on-the-fly for any applicable marker and taxonomic group with optional filtering, formatting and restriction specific for (meta-)barcoding purposes. Also, databases optionally receive a DOI, making them well-documented with meta-data, publicly sharable and citable. Availability and implementation source code: https://www.github.com/molbiodiv/bcdatabaser, webservice: https://bcdatabaser.molecular.eco, documentation: https://molbiodiv.github.io/bcdatabaser.

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Jo, Hyunbin, Dong-Kyun Kim, Kiyun Park, and Ihn-Sil Kwak. "Discrimination of Spatial Distribution of Aquatic Organisms in a Coastal Ecosystem Using eDNA." Applied Sciences 9, no. 17 (August 21, 2019): 3450. http://dx.doi.org/10.3390/app9173450.

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The nonlinearity and complexity of coastal ecosystems often cause difficulties when analyzing spatial and temporal patterns of ecological traits. Environmental DNA (eDNA) monitoring has provided an alternative to overcoming the aforementioned issues associated with classical monitoring. We determined aquatic community taxonomic composition using eDNA based on a meta-barcoding approach that characterizes the general ecological features in the Gwangyang Bay coastal ecosystem. We selected the V9 region of the 18S rDNA gene (18S V9), primarily because of its broad range among eukaryotes. Our results produced more detailed spatial patterns in the study area previously categorized (inner bay, main channel of the bay and outer bay) by Kim et al. (2019). Specifically, the outer bay zone was clearly identified by CCA using genus-level identification of aquatic organisms based on meta-barcoding data. We also found significant relationships between environmental factors. Therefore, eDNA monitoring based on meta-barcoding approach holds great potential as a complemental monitoring tool to identify spatial taxonomic distribution patterns in coastal areas.

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Balech, Bachir, Anna Sandionigi, Caterina Manzari, Emiliano Trucchi, Apollonia Tullo, Flavio Licciulli, Giorgio Grillo, et al. "Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode." PeerJ 6 (June 13, 2018): e4845. http://dx.doi.org/10.7717/peerj.4845.

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Nowadays DNA meta-barcoding is a powerful instrument capable of quickly discovering the biodiversity of an environmental sample by integrating the DNA barcoding approach with High Throughput Sequencing technologies. It mainly consists of the parallel reading of informative genomic fragment/s able to discriminate living entities. Although this approach has been widely studied, it still needs optimization in some necessary steps requested in its advanced accomplishment. A fundamental element concerns the standardization of bioinformatic analyses pipelines. The aim of the present study was to underline a number of critical parameters of laboratory material preparation and taxonomic assignment pipelines in DNA meta-barcoding experiments using the cytochrome oxidase subunit-I (coxI) barcode region, known as a suitable molecular marker for animal species identification. We compared nine taxonomic assignment pipelines, including a custom in-house method, based on Hidden Markov Models. Moreover, we evaluated the potential influence of universal primers amplification bias in qPCR, as well as the correlation between GC content with taxonomic assignment results. The pipelines were tested on a community of known terrestrial invertebrates collected by pitfall traps from a chestnut forest in Italy. Although the present analysis was not exhaustive and needs additional investigation, our results suggest some potential improvements in laboratory material preparation and the introduction of additional parameters in taxonomic assignment pipelines. These include the correct setup of OTU clustering threshold, the calibration of GC content affecting sequencing quality and taxonomic classification, as well as the evaluation of PCR primers amplification bias on the final biodiversity pattern. Thus, careful attention and further validation/optimization of the above-mentioned variables would be required in a DNA meta-barcoding experimental routine.

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ANDERSEN, KENNETH, KAREN LISE BIRD, MORTEN RASMUSSEN, JAMES HAILE, HENRIK BREUNING-MADSEN, KURT H. KJAER, LUDOVIC ORLANDO, M. THOMAS P. GILBERT, and ESKE WILLERSLEV. "Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity." Molecular Ecology 21, no. 8 (September 14, 2011): 1966–79. http://dx.doi.org/10.1111/j.1365-294x.2011.05261.x.

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Terrat, S., S. Dequiedt, W. Horrigue, M. Lelievre, C. Cruaud, N. P. A. Saby, C. Jolivet, et al. "Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding." Heredity 114, no. 5 (October 8, 2014): 468–75. http://dx.doi.org/10.1038/hdy.2014.91.

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Liu, Yin, Xiaowei Li, Yufeng Chen, Guangzhou Geng, Junjie Li, Yongtian Wang, and Lingling Huang. "Imaging-based optical barcoding for relative humidity sensing based on meta-tip." Nanophotonics 11, no. 1 (November 2, 2021): 111–18. http://dx.doi.org/10.1515/nanoph-2021-0529.

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Abstract In a wide range of applications such as healthcare treatment, environmental monitoring, food processing and storage, and semiconductor chip manufacturing, relative humidity (RH) sensing is required. However, traditional fiber-optic humidity sensors face the challenges of miniaturization and indirectly obtaining humidity values. Here, we propose and demonstrate an optical barcode technique by cooperating with RH meta-tip, which can predict the humidity values directly. Such RH meta-tip is composed of fiber-optic sensor based on surface plasmon resonance (SPR) effect and graphene oxide film as humidity sensitizer. While SPR sensor is composed of multimode fiber (MMF) integrated with metallic metasurface. Dynamic time warping (DTW) algorithm is used to obtain the warp path distance (WPD) sequence between the measured reflection spectrum and the spectra of the precalibrated database. The distance sequence is transformed into a pseudo-color barcode, and the humidity value is corresponded to the lowest distance, which can be read by human eyes. The RH measurement depends on the collective changes of the reflection spectrum rather than tracking a single specific resonance peak/dip. This work can open up new doors to the development of a humidity sensor with direct RH recognition by human eyes.

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Byers, Philicity R. M., Rodger C. Evans, Zoë Migicovsky, and Allison K. Walker. "Fungal symbionts of endangered Crocanthemum canadense (Cistaceae) in Nova Scotia." Botany 99, no. 7 (July 2021): 403–19. http://dx.doi.org/10.1139/cjb-2020-0187.

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Crocanthemum canadense (L.) Britton (Cistaceae) is critically imperiled in Nova Scotia. The decline of Nova Scotian Crocanthemum canadense is largely due to the loss of the Annapolis Valley sand barrens habitat. Fungal symbionts may aid in nutrient and water acquisition as well as plant defenses. The role of fungal associations with Crocanthemum canadense is unknown; our goal was to identify fungal symbionts to inform ongoing conservation research. We isolated fungi from eighteen Crocanthemum canadense plants collected from Greenwood, Nova Scotia. Using internal transcribed spacer (ITS) rDNA barcoding of fungal cultures, we identified 58 fungal taxa. ITS2 meta-amplicon barcoding of roots and rhizosphere soil revealed 241 fungi with basidiomycetes accounting for 53.8% of reads. Chaetothyriales sp., Mycetinis scorodonius, Acidomelania panicicola, and Scleroderma citrinum were the most abundant root associates based on meta-amplicon data. We quantified percent root colonization of arbuscular mycorrhizal fungi (AMF) using root staining and microscopy. The average AMF colonization rate of the roots was 29.6% (n = 18). Our research provides a foundation for understanding the fungal community in this declining habitat and the first account of fungal symbionts in the above- and below-ground tissues and rhizosphere of Crocanthemum canadense. Identifying fungi influencing endangered Nova Scotian Crocanthemum canadense is valuable for developing conservation strategies.

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Prodinger, Florian, Hisashi Endo, Yasuhiro Gotoh, Yanze Li, Daichi Morimoto, Kimiho Omae, Kento Tominaga, et al. "An Optimized Metabarcoding Method for Mimiviridae." Microorganisms 8, no. 4 (April 2, 2020): 506. http://dx.doi.org/10.3390/microorganisms8040506.

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Mimiviridae is a group of viruses with large genomes and virions. Ecological relevance of Mimiviridae in marine environments has been increasingly recognized through the discoveries of novel isolates and metagenomic studies. To facilitate ecological profiling of Mimiviridae, we previously proposed a meta-barcoding approach based on 82 degenerate primer pairs (i.e., MEGAPRIMER) targeting the DNA polymerase gene of Mimiviridae. The method detected a larger number of operational taxonomic units (OTUs) in environmental samples than previous methods. However, it required large quantities of DNA and was laborious due to the use of individual primer pairs. Here, we examined coastal seawater samples using varying PCR conditions and purification protocols to streamline the MEGAPRIMER method. Mixing primer pairs in “cocktails” reduced the required amount of environmental DNA by 90%, while reproducing the results obtained by the original protocol. We compared the results obtained by the meta-barcoding approach with quantifications using qPCR for selected OTUs. This revealed possible amplification biases among different OTUs, but the frequency profiles for individual OTUs across multiple samples were similar to those obtained by qPCR. We anticipate that the newly developed MEGAPRIMER protocols will be useful for ecological investigation of Mimiviridae in a larger set of environmental samples.

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Santoferrara, Luciana F., Ewelina Rubin, and George B. Mcmanus. "Global and local DNA (meta)barcoding reveal new biogeography patterns in tintinnid ciliates." Journal of Plankton Research 40, no. 3 (April 12, 2018): 209–21. http://dx.doi.org/10.1093/plankt/fby011.

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Sato, Jun J., Takuya Shimada, Daisuke Kyogoku, Taketo Komura, Shigeru Uemura, Takashi Saitoh, and Yuji Isagi. "Dietary niche partitioning between sympatric wood mouse species (Muridae: Apodemus) revealed by DNA meta-barcoding analysis." Journal of Mammalogy 99, no. 4 (June 14, 2018): 952–64. http://dx.doi.org/10.1093/jmammal/gyy063.

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11

Han, Sang-Hyun, Tae-wook Kim, Jeong-jin Kim, Rak-Won Kim, Jong-baek Kim, Man-woo Kim, Ju-yeol Choi, et al. "A Preliminary Study for Identifying Dietary Resources Using Fecal DNA Meta-barcoding in the Asiatic Black Bears." Korea National Park Research Institute 12, no. 1 (June 30, 2021): 27–36. http://dx.doi.org/10.54406/jnpr.2021.12.1.027.

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12

Comtet, Thierry, Anna Sandionigi, Frédérique Viard, and Maurizio Casiraghi. "DNA (meta)barcoding of biological invasions: a powerful tool to elucidate invasion processes and help managing aliens." Biological Invasions 17, no. 3 (February 10, 2015): 905–22. http://dx.doi.org/10.1007/s10530-015-0854-y.

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Ruiz-Sanchez, Eduardo, Carlos Alonso Maya-Lastra, Victor W. Steinmann, Sergio Zamudio, Eleazar Carranza, Rosa María Murillo, and Jerzy Rzedowski. "Datataxa: a new script to extract metadata sequence information from GenBank, the Flora of Bajío as a case study." Botanical Sciences 97, no. 4 (December 19, 2019): 754–60. http://dx.doi.org/10.17129/botsci.2226.

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Background: GenBank is a public repository that houses millions of nucleotide sequences. Several software have been developed to extract information stored in GenBank. However, none of them are useful to extract and organize GenBank accession based on metadata. We developed a new script called Datataxa, which works to mine GenBank information. The checklist of the Flora del Bajío y de Regiones Adyacentes (FBRA) was used as a case study to apply our script.Questions: How many species occurring in the FBRA have records in GenBank? What percentage of those records have been used for phylogenetic, phylogeographic, phylogenomic, barcoding, genetic diversity, and biogeographic studies?Methods: Datataxa was written in AutoIt Scripting Language in order to facilitate the extraction of information from GenBank. This information was classified in six study categories. A checklist of species published fascicles of FBRA was used as study case to apply our new script, and the previous categories were applied to the FBRA species list.Results: The script allowed us to search for meta information, like publication titles, for 2,558 species that were included in the FBRA. Of these, 1,575 had a least one record in GenBank. A total of 1,322 species were used in phylogenetic studies, followed by barcoding studies (326) and biogeographic studies (298). Phylogenomic (41), phylogeographic (34), and diversity studies (34) were the least represented.Conclusions: Datataxa was useful for mining metadata sequence information from GenBank and can be used with any list of species to get the GenBank accessions’ metadata.

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Pandit, Ramesh, Tasnim Travadi, Sonal Sharma, Chaitanya Joshi, and Madhvi Joshi. "DNA meta‐barcoding using rbcL based mini‐barcode revealed presence of unspecified plant species in Ayurvedic polyherbal formulations." Phytochemical Analysis 32, no. 5 (February 2021): 804–10. http://dx.doi.org/10.1002/pca.3026.

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Chen, Ko-Hsuan, Reid Longley, Gregory Bonito, and Hui-Ling Liao. "A Two-Step PCR Protocol Enabling Flexible Primer Choice and High Sequencing Yield for Illumina MiSeq Meta-Barcoding." Agronomy 11, no. 7 (June 23, 2021): 1274. http://dx.doi.org/10.3390/agronomy11071274.

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High-throughput amplicon sequencing that primarily targets the 16S ribosomal DNA (rDNA) (for bacteria and archaea) and the Internal Transcribed Spacer rDNA (for fungi) have facilitated microbial community discovery across diverse environments. A three-step PCR that utilizes flexible primer choices to construct the library for Illumina amplicon sequencing has been applied to several studies in forest and agricultural systems. The three-step PCR protocol, while producing high-quality reads, often yields a large number (up to 46%) of reads that are unable to be assigned to a specific sample according to its barcode. Here, we improve this technique through an optimized two-step PCR protocol. We tested and compared the improved two-step PCR meta-barcoding protocol against the three-step PCR protocol using four different primer pairs (fungal ITS: ITS1F-ITS2 and ITS1F-ITS4, and bacterial 16S: 515F-806R and 341F-806R). We demonstrate that the sequence quantity and recovery rate were significantly improved with the two-step PCR approach (fourfold more read counts per sample; determined reads ≈90% per run) while retaining high read quality (Q30 > 80%). Given that synthetic barcodes are incorporated independently from any specific primers, this two-step PCR protocol can be broadly adapted to different genomic regions and organisms of scientific interest.

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Mbareche, Hamza, Nathan Dumont-Leblond, Guillaume J. Bilodeau, and Caroline Duchaine. "An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists." Life 10, no. 9 (September 8, 2020): 185. http://dx.doi.org/10.3390/life10090185.

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High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the “dos and don’ts” involved in conducting a precise microbial ecology study.

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YEAGASHI, Sakiko, Hiroki HOSOKAWA, and Kozo WATANABE. "META-BARCODING BASED ASSESSMENT OF WATER ENVIRONEMTAL DNA TO REVEAL ABUNDANCCE OF FRESHWATER INSECTS USING NEXT-GENELATION SEQUENCING." Journal of Japan Society of Civil Engineers, Ser. G (Environmental Research) 73, no. 7 (2017): III_139—III_147. http://dx.doi.org/10.2208/jscejer.73.iii_139.

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JØRGENSEN, TINA, KURT H. KJAER, JAMES HAILE, MORTEN RASMUSSEN, SANNE BOESSENKOOL, KENNETH ANDERSEN, ERIC COISSAC, et al. "Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA Meta-barcoding." Molecular Ecology 21, no. 8 (September 22, 2011): 1980–88. http://dx.doi.org/10.1111/j.1365-294x.2011.05278.x.

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Shahraki, Abdolrazagh Hashemi, Subba Rao Chaganti, and Daniel Heath. "Assessing high-throughput environmental DNA extraction methods for meta-barcode characterization of aquatic microbial communities." Journal of Water and Health 17, no. 1 (October 30, 2018): 37–49. http://dx.doi.org/10.2166/wh.2018.108.

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Abstract The characterization of microbial community dynamics using genomic methods is rapidly expanding, impacting many fields including medical, ecological, and environmental research and applications. One of the biggest challenges for such studies is the isolation of environmental DNA (eDNA) from a variety of samples, diverse microbes, and widely variable community compositions. The current study developed environmentally friendly, user safe, economical, and high throughput eDNA extraction methods for mixed aquatic microbial communities and tested them using 16 s rRNA gene meta-barcoding. Five different lysis buffers including (1) cetyltrimethylammonium bromide (CTAB), (2) digestion buffer (DB), (3) guanidinium isothiocyanate (GITC), (4) sucrose lysis (SL), and (5) SL-CTAB, coupled with four different purification methods: (1) phenol-chloroform-isoamyl alcohol (PCI), (2) magnetic Bead-Robotic, (3) magnetic Bead-Manual, and (4) membrane-filtration were tested for their efficacy in extracting eDNA from recreational freshwater samples. Results indicated that the CTAB-PCI and SL-Bead-Robotic methods yielded the highest genomic eDNA concentrations and succeeded in detecting the core microbial community including the rare microbes. However, our study recommends the SL-Bead-Robotic eDNA extraction protocol because this method is safe, environmentally friendly, rapid, high-throughput and inexpensive.

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Jo, Hyunbin, Bohyung Choi, Kiyun Park, Won-Seok Kim, and Ihn-Sil Kwak. "First Gut Content Analysis of 4th Instar Midge Larvae (Diptera: Chronomidae) In Large-Scale Weirs Using a DNA Meta-Barcoding Approach." International Journal of Environmental Research and Public Health 17, no. 8 (April 21, 2020): 2856. http://dx.doi.org/10.3390/ijerph17082856.

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Chironomidae larvae play an important role in the food chain of river ecosystems in Korea, where it is dominant. However, detailed information on the diet of Chironomidae larvae are still lacking. The purpose of this study was to identify the gut contents of 4th instar larvae of a Chironomidae inhabiting four large-scale weirs (Sejong Weir, Juksan Weir, Gangjeong-Goryeong Weir, and Dalseong Weir) using a DNA meta-barcoding approach. We found that dominant Operational Taxonomic Unit (OUT) was assigned to Paractinolaimus sp. (Nematoda), and the sub-dominant OTU was assigned to Dicrotendipes fumidus (Chironomidae). The most common OTUs among the individuals included phytoplankton, such as Tetrahymena sp., D. armatus, Pseudopediastrum sp., Tetradesmus dimorphus, Biddulphia tridens, and Desmodesmus spp. We calculated the selectivity index (E’) and provided scientific evidence that Chironomidae larvae have a significant preference (E’ > 0.5) for Desmodesmus armatus, E. minima, and T. dimorphus, while it does not show preference for other species found in its gut. Differences in physico-chemical factors, such as water quality, nutrients, Chl-a, and carbon concentrations, resulting from anthropogenic impacts (i.e., construction of large-scale weirs) as well as the particle size of prey organisms (small-sized single cell) and effects of chemicals (chemokinesis) could affect the feeding behavior of Chironomidae larvae.

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Estrada-Franco, José Guillermo, Nadia A. Fernández-Santos, Adeniran A. Adebiyi, María de J. López-López, Jesús A. Aguilar-Durán, Luis M. Hernández-Triana, Sean W. J. Prosser, et al. "Vertebrate-Aedes aegypti and Culex quinquefasciatus (Diptera)-arbovirus transmission networks: Non-human feeding revealed by meta-barcoding and next-generation sequencing." PLOS Neglected Tropical Diseases 14, no. 12 (December 31, 2020): e0008867. http://dx.doi.org/10.1371/journal.pntd.0008867.

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Background Aedes aegypti mosquito-borne viruses including Zika (ZIKV), dengue (DENV), yellow fever (YFV), and chikungunya (CHIKV) have emerged and re-emerged globally, resulting in an elevated burden of human disease. Aedes aegypti is found worldwide in tropical, sub-tropical, and temperate areas. The characterization of mosquito blood meals is essential to understand the transmission dynamics of mosquito-vectored pathogens. Methodology/principal findings Here, we report Ae. aegypti and Culex quinquefasciatus host feeding patterns and arbovirus transmission in Northern Mexico using a metabarcoding-like approach with next-generation deep sequencing technology. A total of 145 Ae. aegypti yielded a blood meal analysis result with 107 (73.8%) for a single vertebrate species and 38 (26.2%) for two or more. Among the single host blood meals for Ae. aegypti, 28.0% were from humans, 54.2% from dogs, 16.8% from cats, and 1.0% from tortoises. Among those with more than one species present, 65.9% were from humans and dogs. For Cx. quinquefasciatus, 388 individuals yielded information with 326 (84%) being from a single host and 63 (16.2%) being from two or more hosts. Of the single species blood meals, 77.9% were from dogs, 6.1% from chickens, 3.1% from house sparrows, 2.4% from humans, while the remaining 10.5% derived from other 12 host species. Among those which had fed on more than one species, 11% were from dogs and humans, and 89% of other host species combinations. Forage ratio analysis revealed dog as the most over-utilized host by Ae. aegypti (= 4.3) and Cx. quinquefasciatus (= 5.6) and the human blood index at 39% and 4%, respectively. A total of 2,941 host-seeking female Ae. aegypti and 3,536 Cx. quinquefasciatus mosquitoes were collected in the surveyed area. Of these, 118 Ae. aegypti pools and 37 Cx. quinquefasciatus pools were screened for seven arboviruses (ZIKV, DENV 1–4, CHIKV, and West Nile virus (WNV)) using qRT-PCR and none were positive (point prevalence = 0%). The 95%-exact upper limit confidence interval was 0.07% and 0.17% for Ae. aegypti and Cx. quinquefasciatus, respectively Conclusions/significance The low human blood feeding rate in Ae. aegypti, high rate of feeding on mammals by Cx. quinquefasciatus, and the potential risk to transmission dynamics of arboviruses in highly urbanized areas of Northern Mexico is discussed.

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Blaxter, Mark L. "The promise of a DNA taxonomy." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359, no. 1444 (April 29, 2004): 669–79. http://dx.doi.org/10.1098/rstb.2003.1447.

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Not only is the number of described species a very small proportion of the estimated extant number of taxa, but it also appears that all concepts of the extent and boundaries of ‘species’ fail in many cases. Using conserved molecular sequences it is possible to define and diagnose molecular operational taxonomic units (MOTU) that have a similar extent to traditional ‘species’. Use of a MOTU system not only allows the rapid and effective identification of most taxa, including those not encountered before, but also allows investigation of the evolution of patterns of diversity. A MOTU approach is not without problems, particularly in the area of deciding what level of molecular difference defines a biologically relevant taxon, but has many benefits. Molecular data are extremely well suited to re–analysis and meta–analysis, and data from multiple independent studies can be readily collated and investigated by using new parameters and assumptions. Previous molecular taxonomic efforts have focused narrowly. Advances in high–throughput sequencing methodologies, however, place the idea of a universal, multi–locus molecular barcoding system in the realm of the possible.

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Kumar, Niraj. "Application of 16 rRNA Gene of V3-V4 Region for Meta Barcoding of Bacterial Community in High Density Population of Eastern India." Bioscience Biotechnology Research Communications 13, no. 4 (December 25, 2020): 1871–78. http://dx.doi.org/10.21786/bbrc/13.4/36.

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Snyder, Susan R., Alessandra M. Favoretto, James H. Derzon, Robert H. Christenson, Stephen E. Kahn, Colleen S. Shaw, Rich Ann Baetz, et al. "Effectiveness of barcoding for reducing patient specimen and laboratory testing identification errors: A Laboratory Medicine Best Practices systematic review and meta-analysis." Clinical Biochemistry 45, no. 13-14 (September 2012): 988–98. http://dx.doi.org/10.1016/j.clinbiochem.2012.06.019.

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25

Wolińska, Agnieszka, Agnieszka Kuźniar, and Anna Gałązka. "Biodiversity in the Rhizosphere of Selected Winter Wheat (Triticum aestivum L.) Cultivars—Genetic and Catabolic Fingerprinting." Agronomy 10, no. 7 (July 2, 2020): 953. http://dx.doi.org/10.3390/agronomy10070953.

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The main goal of the study was to determine the biodiversity of bacteria and their metabolic profile in the rhizosphere of four winter wheat (Triticum aestivum L.) varieties (Hondia, Nordkap, Rotax, Tytanika) cultivated in Haplic Podzol soil in a no-tillage system. Two techniques, i.e., next generation sequencing (NGS, meta-barcoding of 16S rRNA community) and community level physiological profiling (CLPP), were applied to obtain a holistic picture of biodiversity. The basic soil chemical parameters (acidity, redox potential, carbon content, forms of nitrogen, and phosphorus) were also determined. It was found that the rhizospheric microbiome (at the genus level) of cv. Hondia and Rotax were significantly different from that present in the other cultivars studied. The CLPP technique demonstrated that microbial metabolic activity depended on both the type of substrate and wheat cultivars. Carbohydrates and carboxylic acids were the most easily utilized compounds in all rhizospheric soils. The principal component analysis (PCA) evidenced that the rhizospheric soils of Rotax and Nordkap were characterized by a higher functional activity (strong correlation with the Shannon-Wiener index, the Richness index, and utilization of hydrocarbons) than those of Hondia and Tytanika.

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Li, Yanze, Pascal Hingamp, Hiroyasu Watai, Hisashi Endo, Takashi Yoshida, and Hiroyuki Ogata. "Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters." Viruses 10, no. 9 (September 13, 2018): 496. http://dx.doi.org/10.3390/v10090496.

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“Megaviridae” is a proposed family of giant viruses infecting unicellular eukaryotes. These viruses are ubiquitous in the sea and have impact on marine microbial community structure and dynamics through their lytic infection cycle. However, their diversity and biogeography have been poorly characterized due to the scarce detection of Megaviridae sequences in metagenomes, as well as the limitation of reference sequences used to design specific primers for this viral group. Here, we propose a set of 82 degenerated primers (referred to as MEGAPRIMER), targeting DNA polymerase genes (polBs) of Megaviridae. MEGAPRIMER was designed based on 921 Megaviridae polBs from sequenced genomes and metagenomes. By applying this primer set to environmental DNA meta-barcoding of a coastal seawater sample, we report 5595 non-singleton operational taxonomic units (OTUs) of Megaviridae at 97% nucleotide sequence identity. The majority of the OTUs were found to form diverse clades, which were phylogenetically distantly phylogenetically related to known viruses such as Mimivirus. The Megaviridae OTUs detected in this study outnumber the giant virus OTUs identified in previous individual studies by more than an order of magnitude. Hence, MEGAPRIMER represents a useful tool to study the diversity of Megaviridae at the population level in natural environments.

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Zamoroka, A. M., D. V. Semaniuk, V. Yu Shparyk, T. V. Mykytyn, and S. V. Skrypnyk. "Taxonomic Position of Anastrangalia reyi and A. sequensi (Coleoptera, Cerambycidae) Based on Molecular and Morphological Data." Vestnik Zoologii 53, no. 3 (June 1, 2019): 209–26. http://dx.doi.org/10.2478/vzoo-2019-0021.

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Abstract Anastrangalia reyi (Heyden, 1889) and Anastrangalia sequensi (Reitter, 1898) are morphologically similar species described in late of XIX century. The recent barcoding revealed that A. reyi is almost identical to another species, Anastrangalia dubia (Scopoli, 1763), by the sequence of nucleotides in cytochrome C oxidase subunit I (COI). Consequently, the taxonomic position of these species is unclear. We have conducted a comprehensive meta-analysis of available data of COI sequences combined with a study of morphological characters of the male genitalia of A. reyi, A. sequensi and A. dubia. Based on 87 sequenced samples we built well-resolved phylogenetic maximum likelihood tree. We found the clades of A. dubia, A. reyi and A. sequensi to be closely related and arranged in the dense cluster. Despite this, numerous cases of introgressive hybridization of A. reyi and A. dubia were identified, indicating an inadequate reproductive barrier between them. The study of morphological features of male genitalia of A. reyi, A. sequensi and A. dubia shows minor differences between them. Based on these facts and the results of the phylogenetic analysis we propose to consider A. reyi and A. sequensi to be subspecies of A. dubia.

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Metfies, Katja, Johanna Hessel, Robin Klenk, Wilhelm Petersen, Karen Helen Wiltshire, and Alexandra Kraberg. "Uncovering the intricacies of microbial community dynamics at Helgoland Roads at the end of a spring bloom using automated sampling and 18S meta-barcoding." PLOS ONE 15, no. 6 (June 22, 2020): e0233921. http://dx.doi.org/10.1371/journal.pone.0233921.

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Heo, Young-Mok, Hanbyul Lee, Sun-Lul Kwon, Yeonjae Yoo, Dongjun Kim, Sang-Il Han, Aslan-Hwanhwi Lee, Changmu Kim, Gyu-Hyeok Kim, and Jae-Jin Kim. "Influence of Tree Vegetation on Soil Microbial Communities in Temperate Forests and Their Potential as a Proactive Indicator of Vegetation Shift Due to Climate Change." Sustainability 12, no. 24 (December 18, 2020): 10591. http://dx.doi.org/10.3390/su122410591.

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Unexpected vegetation shift is a serious problem caused by climate change, resulting in considerable damage to local communities. It is necessary to be continuously monitored, and the soil microbial community is expected to reflect the pressure on forest ecosystems due to climate change. We investigated soil bacterial and fungal communities in Odaesan at a four-year interval through eDNA meta-barcoding and analyzed the compositional and functional differences between forest types (Mongolian oak (Quercus mongolica) forest with and without Manchurian firs (Abies holophylla)) and sampling years. As a result, denitrifiers predominated in the presence of Manchurian firs, but there was no difference in the influence of climate change by forest type. Although tree vegetation remained stable, the microbial communities significantly changed over four years. This result demonstrates that climate change significantly shifts the microbial communities, even if not enough to trigger a vegetation shift, thus a microbial indicator can be developed to assess the press disturbance accumulated on the forest ecosystem. Through this study, we identified the influence of Manchurian firs and that of climate change on soil microbial communities in temperate forests and demonstrated the potential of the microbial community as a proactive indicator of vegetation shift due to climate change.

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Cloutier, Véronique B., Yves Piché, J. André Fortin, Jean A. Bérubé, Hélène Glémet, and André Desrochers. "A novel approach for tracing mycophagous small mammals and documenting their fungal diets." Botany 97, no. 9 (September 2019): 475–785. http://dx.doi.org/10.1139/cjb-2018-0222.

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We developed a method combining passive baiting (animals that are not trapped) with DNA meta-barcoding of the feces acquired, to study fungi in the diet of small mammals. Mammal and fungal species were identified using genomic DNA of 596 fecal samples collected in five regions of the eastern Canadian boreal forest. For identification of the small mammal species, the cytochrome b region was used. A total of eight species of small mammals displayed hypogeous fungi consumption, with northern flying squirrels (Glaucomys sabrinus) and red-backed voles (Myodes gapperi) as the top consumers. For identification of their fungal diets, the ribosomal internal transcribed spacer (ITS) region was used. We recovered 722 taxa of Ascomycota, 429 Basidiomycota, 81 Zygomycota, 4 Chytridiomycota, 1 Glomeromycota, and 44 unidentified fungal taxa. Of these, 28 were hypogeous sequestrate fungi (underground fructification), which presumably are dug out by small mammals for consumption. Otherwise, for the remaining fungi [epigeous (above ground fructification) or microscopic fungal species], it is unclear which ones are selected by the animal as a dietary source or result from incidental contamination. Our paper presents a promising approach for tracing mycophagy in small mammals, and our results suggest that fungal diversity is important for the diet of some small mammals.

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Wolińska, Agnieszka, Kinga Włodarczyk, Agnieszka Kuźniar, Anna Marzec-Grządziel, Jarosław Grządziel, Anna Gałązka, and Łukasz Uzarowicz. "Soil Microbial Community Profiling and Bacterial Metabolic Activity of Technosols as an Effect of Soil Properties following Land Reclamation: A Case Study from the Abandoned Iron Sulphide and Uranium Mine in Rudki (South-Central Poland)." Agronomy 10, no. 11 (November 16, 2020): 1795. http://dx.doi.org/10.3390/agronomy10111795.

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The aims of the study were (1) to recognize the structure of bacteria diversity in Technosols developed from mine spoils containing iron (Fe) sulphides with the use of culture-independent technique, and (2) to determine microbial metabolic activities, in the context of their potential to be an adequate indicators of soil properties being the consequence of land reclamation. The study site was located in the vicinity of the abandoned Fe sulphide and uranium mine in Rudki village (Holy Cross Mts., Poland). Three soil profiles with different chemical properties (pH, content of carbonates, soil salinity, content of total organic carbon and total nitrogen) were studied. Biodiversity was determined with the use of meta-barcoding of 16S rRNA community profiling analysis based on the hypervariable V3-V4 region of 16S rRNA gene (MiSeq, Illumina). The catabolic fingerprinting of soil microbial communities was evaluated with the use of Biolog®EcoPlates™ System. It was evidenced that changes in microbial structure and their metabolic activity were the consequence of a combined effect of both the soil depth and soil chemical properties being the final result of reclamation process. Consequently, microbial indicators (from phyla to genera level) indirectly testifying about success or ineffectiveness of reclamation in technogenic soils were recommended. To our best knowledge, the present study is the first insight into Polish Technosols biodiversity and catabolic activity.

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Thanni, Bolaji, Roel Merckx, Pieterjan De Bauw, Margaux Boeraeve, Gerrit Peeters, Stefan Hauser, and Olivier Honnay. "Spatial variability and environmental drivers of cassava—arbuscular mycorrhiza fungi (AMF) associations across Southern Nigeria." Mycorrhiza 32, no. 1 (January 2022): 1–13. http://dx.doi.org/10.1007/s00572-021-01058-x.

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AbstractCassava, forming starch-rich, tuberous roots, is an important staple crop in smallholder farming systems in sub-Saharan Africa. Its relatively good tolerance to drought and nutrient-poor soils may be partly attributed to the crop’s association with arbuscular mycorrhiza fungi (AMF). Yet insights into AMF-community composition and richness of cassava, and knowledge of its environmental drivers are still limited. Here, we sampled 60 cassava fields across three major cassava-growing agro-ecological zones in Nigeria and used a DNA meta-barcoding approach to quantify large-scale spatial variation and evaluate the effects of soil characteristics and common agricultural practices on AMF community composition, richness and Shannon diversity. We identified 515 AMF operational taxonomic units (OTUs), dominated by Glomus, with large variation across agro-ecological zones, and with soil pH explaining most of the variation in AMF community composition. High levels of soil available phosphorus reduced OTU richness without affecting Shannon diversity. Long fallow periods (> 5 years) reduced AMF richness compared with short fallows, whereas both zero tillage and tractor tillage reduced AMF diversity compared with hoe tillage. This study reveals that the symbiotic relationship between cassava and AMF is strongly influenced by soil characteristics and agricultural management and that it is possible to adjust cassava cultivation practices to modify AMF diversity and community structure. Graphical abstract

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Balaban, Metin, Shahab Sarmashghi, and Siavash Mirarab. "APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments." Systematic Biology 69, no. 3 (September 23, 2019): 566–78. http://dx.doi.org/10.1093/sysbio/syz063.

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Abstract Placing a new species on an existing phylogeny has increasing relevance to several applications. Placement can be used to update phylogenies in a scalable fashion and can help identify unknown query samples using (meta-)barcoding, skimming, or metagenomic data. Maximum likelihood (ML) methods of phylogenetic placement exist, but these methods are not scalable to reference trees with many thousands of leaves, limiting their ability to enjoy benefits of dense taxon sampling in modern reference libraries. They also rely on assembled sequences for the reference set and aligned sequences for the query. Thus, ML methods cannot analyze data sets where the reference consists of unassembled reads, a scenario relevant to emerging applications of genome skimming for sample identification. We introduce APPLES, a distance-based method for phylogenetic placement. Compared to ML, APPLES is an order of magnitude faster and more memory efficient, and unlike ML, it is able to place on large backbone trees (tested for up to 200,000 leaves). We show that using dense references improves accuracy substantially so that APPLES on dense trees is more accurate than ML on sparser trees, where it can run. Finally, APPLES can accurately identify samples without assembled reference or aligned queries using kmer-based distances, a scenario that ML cannot handle. APPLES is available publically at github.com/balabanmetin/apples.

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Liu, Gang, Aaron B. A. Shafer, Xiaolong Hu, Linhai Li, Yu Ning, Minghao Gong, Lijuan Cui, et al. "Meta-barcoding insights into the spatial and temporal dietary patterns of the threatened Asian Great Bustard (Otis tarda dybowskii) with potential implications for diverging migratory strategies." Ecology and Evolution 8, no. 3 (January 8, 2018): 1736–45. http://dx.doi.org/10.1002/ece3.3791.

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Katsi, Pavlina, Ioanna S. Kosma, Sofia Michailidou, Anagnostis Argiriou, Anastasia V. Badeka, and Michael G. Kontominas. "Characterization of Artisanal Spontaneous Sourdough Wheat Bread from Central Greece: Evaluation of Physico-Chemical, Microbiological, and Sensory Properties in Relation to Conventional Yeast Leavened Wheat Bread." Foods 10, no. 3 (March 17, 2021): 635. http://dx.doi.org/10.3390/foods10030635.

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In the present study, both yeast leavened bread (YLB) and artisanal sourdough wheat bread (SDB) were prepared. The physico-chemical, microbiological, and sensory properties of breads were monitored as a function of storage time (T = 25 °C). As expected, the titratable acidity (TA) values of SDB were higher than those of YLB. The aroma profile of SDB was similar to that of YLB, including classes of compounds such as alcohols, aldehydes, ketones, esters, organic acids, terpenes, and sulfur compounds; however, the concentrations between the two were different. Aroma deterioration of bread during storage was partly related to the loss of several volatiles. Texture and sensory analysis showed that SDB was harder, less elastic, but richer in aroma and light sour taste than YLB. Mold growth was apparent when the population of yeasts/molds reached approximately 4 log cfu/g. This yeast/mold count was reached on days 4–5 for YLB and day 18 + for SDB. A 16S amplicon meta-barcoding analysis showed that the bacterial profile of SDB was dominated by a single genus, (Lactobacillus). Analysis of the eukaryotic load showed that at the genus level, Saccharomyces and Alternaria were the most abundant genera, independently of the gene sequenced (18S or ITS). Based primarily on mold growth and texture data, which proved to be the most sensitive quality parameters, the shelf life was ca. 4–5 days for YLB and 10 days for SDB.

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Cuijvers, Kathleen, Steven Van Den Heuvel, Cristian Varela, Mark Rullo, Mark Solomon, Simon Schmidt, and Anthony Borneman. "Alterations in Yeast Species Composition of Uninoculated Wine Ferments by the Addition of Sulphur Dioxide." Fermentation 6, no. 2 (June 23, 2020): 62. http://dx.doi.org/10.3390/fermentation6020062.

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Uninoculated wine fermentations are conducted by a consortium of wine yeast and bacteria that establish themselves either from the grape surface or from the winery environment. Of the additives that are commonly used by winemakers, sulphur dioxide (SO2) represents the main antimicrobial preservative and its use can have drastic effects on the microbial composition of the fermentation. To investigate the effect of SO2 on the resident yeast community of uninoculated ferments, Chardonnay grape juice from 2018 and 2019 was treated with a variety of SO2 concentrations ranging up to 100 mg/L and was then allowed to undergo fermentation, with the yeast community structure being assessed via high-throughput meta-barcoding (phylotyping). While the addition of SO2 was shown to select against the presence of many species of non-Saccharomyces yeasts, there was a clear and increasing selection for the species Hanseniaspora osmophila as concentrations of SO2 rose above 40 mg/L in fermentations from both vintages. Chemical analysis of the wines resulting from these treatments showed significant increases in acetate esters, and specifically the desirable aroma compound 2-phenylethyl acetate, that accompanied the increase in abundance of H. osmophila. The ability to modulate the yeast community structure of an uninoculated ferment and the resulting chemical composition of the final wine, as demonstrated in this study, represents an important tool for winemakers to begin to be able to influence the organoleptic profile of uninoculated wines.

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Zhang, Hai-Guang, Min-Hua Lv, Wen-Bo Yi, Wei-Bing Zhu, and Wen-Jun Bu. "Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genusCletus(Hemiptera: Coreidae) and the meta-analysis ofCOIdata from previous phylogeographical studies." Molecular Ecology Resources 17, no. 2 (August 20, 2016): 314–23. http://dx.doi.org/10.1111/1755-0998.12571.

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Parlapani, Foteini F., Sofia Michailidou, Konstantinos Pasentsis, Anagnostis Argiriou, Grigorios Krey, and Ioannis S. Boziaris. "A meta-barcoding approach to assess and compare the storage temperature-dependent bacterial diversity of gilt-head sea bream ( Sparus aurata ) originating from fish farms from two geographically distinct areas of Greece." International Journal of Food Microbiology 278 (August 2018): 36–43. http://dx.doi.org/10.1016/j.ijfoodmicro.2018.04.027.

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Mumme, Hope L., Swati S. Bhasin, Beena E. Thomas, Deborah DeRyckere, Sharon M. Castellino, Douglas K. Graham, Sunil S. Raikar, and Manoj Bhasin. "Single Cell RNA Sequencing Driven Characterization of Rare B/Myeloid and T/Myeloid Mixed Phenotype Acute Leukemia." Blood 138, Supplement 1 (November 5, 2021): 3455. http://dx.doi.org/10.1182/blood-2021-153776.

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Abstract Introduction: Pediatric mixed phenotype acute leukemia (MPAL), a rare subgroup of leukemia, contains features of both myeloid and lymphoid lineage blasts, which makes the disease more difficult to diagnose/treat. More information is needed to understand the origins of the major pediatric MPAL subtypes, B/Myeloid (B-MPAL) and T/Myeloid (T-MPAL), and how they relate to other leukemias. Single-cell RNA sequencing (scRNA-seq) analysis of bone marrow (BM) can provide in-depth information about the leukemia microenvironment and reveal differences/similarities between MPAL subtypes and other types of leukemia that could be exploited to develop novel diagnostics/therapies. Methods: We analyzed ~16,000 cells from five pediatric MPAL BM samples to generate a transcriptomic landscape of B-MPAL and T-MPAL blasts and associated microenvironment cells. Samples collected at the time of diagnosis (Dx) were used to generate scRNA-Seq data using a droplet-based barcoding technique (Panigrahy et al. JCI 2019, Tellechea et al. JID, 2020). After data normalization, cell clusters were identified using principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) approach (Becht et al. Nat. Biotech 2018). Meta-analysis was performed using single cell samples from ongoing studies in the Bhasin lab (Bhasin, et al. Blood 2020 (ASH), Thomas et al. Blood 2020 (ASH)) and publicly available single cell data from GEO biorepository. Unsupervised analysis using UMAP and PCA was performed to determine the overall relationship among B-MPAL, T-MPAL and other leukemias (acute myeloid leukemia (AML), B-cell acute lymphoblastic leukemia (B-ALL), T-cell ALL (T-ALL)). Supervised differentially expressed gene (DEG) analysis was performed to identify B- and T- MPAL blast cell signatures (P value < 0.001 and log2 FC > 0.5). Transcriptomic profiles in MPAL samples and normal BM stem and immune cells were compared using data from the Human Cell Atlas Data Portal (humancellatlas.org). Gene set enrichment analysis (GSEA) was performed, and significantly enriched pathways were compared in MPAL subtypes (P value < 0.001). Results: PCA analysis showed transcriptome similarity between B-MPAL and both B-ALL and AML, while T-MPAL transcriptome correlated with T-ALL and AML (Fig. 1A). B- and T-MPAL subtype blasts clustered separately from each other in UMAP analyses, with T-MPAL blasts clustering with T-ALL blasts, and B-MPAL somewhat overlapping with B-ALL blasts. Subtype DEG analysis of leukemia blasts and healthy BM revealed distinct significantly upregulated gene signatures in B-MPAL (YBX3, SOCS2, BCL11A, and HIST1H1C) and T-MPAL (ITM2A, HPGD, PDLIM1, and TRDC) blasts (Fig. 1B). Pathway analysis showed upregulated gene activity related to TNFA signaling via NFKB, B-cell survival, and the AP1, FRA, and NGF transcription factors in B-MPAL blasts. In contrast, IL-17 and IL-12, T-cell apoptosis, and Stathmin pathways were upregulated in T-MPAL blasts (Fig. 1C). T-MPAL T-cells also expressed higher levels of T-cell exhaustion markers compared to T-cells in B-MPAL samples and healthy bone marrow. After filtering out genes that are significantly expressed in immune cells, we identified genes that are differentially expressed at diagnosis in MPAL blasts from patients that relapsed after treatment (Dx1) versus patients that achieved remission (Dx2). These genes are potential prognostic markers for B-MPAL and T-MPAL relapse/remission. These include MDM2 and NEIL1 from Dx1 and FOSL2 and CDKN1A in Dx2 B-MPAL blasts. In T-MPAL, expression of HES4 and SPINK2 is associated with Dx1 blasts and GNAQ and ITGA4 with Dx2 blasts. Pathway enrichment analysis on B-MPAL blasts revealed upregulation of interferon gamma and PD-1 signaling in Dx1 samples and increased HSP27 and Cell Cycle pathways in the Dx2 subset. T-MPAL Dx1 associated pathways included prostaglandin synthesis and IL-17, while cell-cell junction and extracellular matrix interactions were increased in T-MPAL Dx2 samples (Fig. 1D). Conclusion: Single-cell profiling was used to characterize the molecular landscapes of MPAL blasts and the bone marrow microenvironment and identified gene signatures and pathways that are specifically enriched in B- and T-MPAL subtypes. Figure 1 Figure 1. Disclosures DeRyckere: Meryx: Other: Equity ownership. Graham: Meryx: Membership on an entity's Board of Directors or advisory committees, Other: Equity ownership.

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Kholilah, Nenik, Norma Afiati, Subagiyo Subagiyo, and Retno Hartati. "Meta-analysis of Indonesian Octopus laqueus Kaneko & Kubodera 2005 (Cephalopoda: Octopodidae) using Mt-DNA COI as Genetic Marker." Jurnal Kelautan Tropis 24, no. 1 (February 12, 2021): 7–14. http://dx.doi.org/10.14710/jkt.v24i1.10190.

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O. laqueus was first discovered not long ago in 2005 in the Ryuku Islands, Japan. Its geographical distribution and molecular identification are therefore still rarely. Nucleotide sequences based on mt-DNA COI for O. laqueus that have been uploaded in the GenBank until before this study was carried out were only six sequences. Since DNA barcoding of mt-DNA COI has some advantageous characteristics, this study aimed to analyse the genetic difference of Indonesian O. laqueus to the data available in the GenBank. Samples were collected in 2019 - 2020 from Karimunjawa (n=16) and Bangka-Belitung (n=2). The mt-DNA COI was extracted using 10% chelex methods, PCR amplified using Folmer’s primer and sequenced in Sanger methods. Pairwise alignment and genetic distance were carried out in MEGA-X, whereas the phylogenetic tree was reconstructed using Bayesian methods. BLAST identification resulted in 685 bp with a range of 92,07-99,24 percentages of identity. The genetic mean pair-wise distances within-clade were 0,002 and 0,006, whilst the distance between the clade was 0.0883. Combining the suggestion with the ITF current, it is concluded that O. laqueus taken from Karimunjawa raised from the same species as those in Malaysia (MN711655) and Japan (AB302176). Specimens from Bangka-Belitung were suggested came from different species, as they were separated into the second clade by 8.83%. One single sample from Japan (AB430543) which laid outside the two clades by 11.63%-11.38% was also suggested to represent a different species. Overall, this study opens to various further studies on O. laqueus using other loci of genetic markers.

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Zhu, Shuang, Qiaozhen Liu, Simin Qiu, Jiangpeng Dai, and Xiaoxia Gao. "DNA barcoding: an efficient technology to authenticate plant species of traditional Chinese medicine and recent advances." Chinese Medicine 17, no. 1 (September 28, 2022). http://dx.doi.org/10.1186/s13020-022-00655-y.

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AbstractTraditional Chinese medicine (TCM) plays an important role in the global traditional health systems. However, adulterated and counterfeit TCM is on the rise. DNA barcoding is an effective, rapid, and accurate technique for identifying plant species. In this study, we collected manuscripts on DNA barcoding published in the last decade and summarized the use of this technique in identifying 50 common Chinese herbs listed in the Chinese pharmacopoeia. Based on the dataset of the major seven DNA barcodes of plants in the NCBI database, the strengths and limitations of the barcodes and their derivative barcoding technology, including single-locus barcode, multi-locus barcoding, super-barcoding, meta-barcoding, and mini-barcoding, were illustrated. In addition, the advances in DNA barcoding, particularly identifying plant species for TCM using machine learning technology, are also reviewed. Finally, the selection process of an ideal DNA barcoding technique for accurate identification of a given TCM plant species was also outlined.

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Holdaway, Robert, Jamie Wood, Ian Dickie, Kate Orwin, Peter Bellingham, Sarah Richardson, Phil Lyver, Puke Timoti, and Thomas Buckley. "Using DNA meta barcoding to assess New Zealand's terrestrial biodiversity." New Zealand Journal of Ecology 41, no. 2 (2017). http://dx.doi.org/10.20417/nzjecol.41.28.

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Sternes, Peter R., Danna Lee, Dariusz R. Kutyna, and Anthony R. Borneman. "A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation." GigaScience 6, no. 7 (June 8, 2017). http://dx.doi.org/10.1093/gigascience/gix040.

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Wylezich, Claudia, and Dirk Höper. "Meta-Ribosomalomics: RNA Sequencing Is an Unbiased Method for Parasite Detection of Different Sample Types." Frontiers in Microbiology 12 (June 21, 2021). http://dx.doi.org/10.3389/fmicb.2021.614553.

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In this perspective article, we review the past use of ribosomal sequences to address scientific and diagnostic questions. We highlight a variety of sequencing approaches including metagenomics and DNA barcoding and their different demands and requirements. Meta-ribosomalomics is introduced as an unbiased approach to exploit high-throughput sequencing datasets for eukaryotic and prokaryotic ribosomal sequences. Prerequisites, benefits, drawbacks, and future perspectives are elaborated and compared to other sequencing approaches.

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Buchner, Dominik, Till-Hendrik Macher, and Florian Leese. "APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA Meta-barcoding data." Bioinformatics, August 27, 2022. http://dx.doi.org/10.1093/bioinformatics/btac588.

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Abstract Summary DNA metabarcoding is an emerging approach to assess and monitor biodiversity worldwide and consequently the number and size of data sets increases exponentially. To date no published DNA metabarcoding data processing pipeline exists that is i) platform independent, ii) easy to use (incl. GUI), iii) fast (does scale well with dataset size), and iv) complies with data protection regulations of e.g., environmental agencies. The presented pipeline APSCALE meets these requirements and handles the most common tasks of sequence data processing, such as paired-end merging, primer trimming, quality filtering, clustering and denoising of any popular metabarcoding marker, such as ITS (internal transcribed spacer), 16S, or COI (cytochrome c oxidase subunit I). APSCALE comes in a command-line and a GUI version. The latter provides the user with additional summary statistics options and links to GUI-based downstream applications. Availability APSCALE is written in Python, a platform-independent language, and integrates functions of the open-source tools, VSEARCH (Rognes et al. 2016), cutadapt (Martin et al, 2011) and LULU (Frøslev et al. 2017). All modules support multithreading to allow fast processing of larger DNA metabarcoding datasets. Further information, and troubleshooting are provided on the respective GitHub pages for the command line version (https://github.com/DominikBuchner/apscale) and the GUI-based version (https://github.com/TillMacher/apscale_gui), including a detailed tutorial. Supplementary information Supplementary data are available at Bioinformatics online.

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Mahima, Karthikeyan, Koppala Narayana Sunil Kumar, Kanakarajan Vijayakumari Rakhesh, Parameswaran Sathiya Rajeswaran, Ashutosh Sharma, and Ramalingam Sathishkumar. "Advancements and future prospective of DNA barcodes in the herbal drug industry." Frontiers in Pharmacology 13 (October 21, 2022). http://dx.doi.org/10.3389/fphar.2022.947512.

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Ethnopharmacological relevance: The past couple of decades have witnessed the global resurgence of medicinal plants in the field of herbal-based health care. Increased consumption of medicinal plants and their derivative products is the major cause of the adulteration issues in herbal industries. As a result, the quality of herbal products is affected by spurious and unauthorized raw materials. Recent development in molecular plant identification using DNA barcodes has become a robust methodology to identify and authenticate the adulterants in herbal samples. Hence, rapid and accurate identification of medicinal plants is the key to success for the herbal industry. Aim of the study: This paper provides a comprehensive review of the application of DNA barcoding and advanced technologies that have emerged over the past 10 years related to medicinal plant identification and authentication and the future prospects of this technology.Materials and methods: Information on DNA barcodes was compiled from scientific databases (Google Scholar, Web of Science, SciFinder and PubMed). Additional information was obtained from books, Ph.D. thesis and MSc. Dissertations.Results: Working out an appropriate DNA barcode for plants is challenging; the single locus-based DNA barcodes (rbcL, ITS, ITS2, matK, rpoB, rpoC, trnH-psbA) to multi-locus DNA barcodes have become the successful species-level identification among herbal plants. Additionally, multi-loci have become efficient in the authentication of herbal products. Emerging advances in DNA barcoding and related technologies such as next-generation sequencing, high-resolution melting curve analysis, meta barcodes and mini barcodes have paved the way for successful herbal plant/samples identification.Conclusion: DNA barcoding needs to be employed together with other techniques to check and rationally and effectively quality control the herbal drugs. It is suggested that DNA barcoding techniques combined with metabolomics, transcriptomics, and proteomics could authenticate the herbal products. The invention of simple, cost-effective and improved DNA barcoding techniques to identify herbal drugs and their associated products of medicinal value in a fool-proof manner will be the future thrust of Pharmacopoeial monograph development for herbal drugs.

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Landinez-Torres, Angela, Simona Panelli, Anna Maria Picco, Francesco Comandatore, Solveig Tosi, and Enrica Capelli. "A meta-barcoding analysis of soil mycobiota of the upper Andean Colombian agro-environment." Scientific Reports 9, no. 1 (July 12, 2019). http://dx.doi.org/10.1038/s41598-019-46485-1.

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Sickel, Wiebke, Markus J. Ankenbrand, Gudrun Grimmer, Andrea Holzschuh, Stephan Härtel, Jonathan Lanzen, Ingolf Steffan-Dewenter, and Alexander Keller. "Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach." BMC Ecology 15, no. 1 (July 22, 2015). http://dx.doi.org/10.1186/s12898-015-0051-y.

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Laha, Rama Chandra, Surajit De Mandal, Lalhmanghai Ralte, Laldinfeli Ralte, Nachimuthu Senthil Kumar, Guruswami Gurusubramanian, Ramalingam Satishkumar, Raja Mugasimangalam, and Nagesh Aswathnarayana Kuravadi. "Meta-barcoding in combination with palynological inference is a potent diagnostic marker for honey floral composition." AMB Express 7, no. 1 (June 24, 2017). http://dx.doi.org/10.1186/s13568-017-0429-7.

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YANG Liping, 杨丽平, 常会会 CHANG Huihui, 李杰 LI Jie, 张智斌 ZHANG Zhibin, and 黄原 HUANG Yuan. "Study of the biodiversity in intestinal symbiotic fungi in grasshoppers species by using DNA meta-barcoding." Acta Ecologica Sinica 37, no. 20 (2017). http://dx.doi.org/10.5846/stxb201606211216.

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